Modules of algorithms of calculations

Diesel

It is a base computational module and it contains class for calculating of molecular dynamic, that includes Verlet, Leapfrog and other integrators.

class kvazar.diesel.Diesel(struct, method, integrator={'name': 'VELVERLET'}, log_to_file=False)[source]

Module for molecular dynamic calculation. To initialize it, you have to set structure and method.

check_pbc()[source]

If any atoms are out of box, method will try to return them back.

dissipative_step()[source]

The Velocity Verlet Algorithm.

get_forces()[source]

The calculation of forces acting on atoms.

init_cutoff(r_in, r_out)[source]

Van-der-Vaals forces cutoff at some distance.

leapfrog_berendsen_step()[source]

The Verlet Leapfrog Algorithm with Berendsen Thermostat.

leapfrog_nosehoover_step()[source]

The Verlet Leapfrog Algorithm with Berendsen Thermostat.

leapfrog_step()[source]

The Verlet Leapfrog Algorithm.

run(time_steps)[source]

Runs calculations as many times as it follows from conditions.

simulation(output, period, max_time, config=None, rec_type='w')[source]

It writes structure characteristics and monitoring values in output file.

use_pbc(pbc_box)[source]

Periodic boundary conditions can be used in calculations. Geometry of pbc box should be setted.

velocity_verlet_step()[source]

The Velocity Verlet Algorithm.

verlet_step()[source]

The Basic Verlet Algorithm.

Periodic Boundary Conditions

class kvazar.boxcell.BoxCell(coords, r_in, r_out, box)[source]

It’s a class that realizes periodic boundary conditions.

build_cells(coords)[source]

This method checks sizes of structure and raises exception if structure is bigger than periodic box. Else it returns list of atom names for each part of periodic box.

calc_neighbours(coords, a, b)[source]

It builds periodic box and then update cutoff lists, if needed.

time_to_update(coords, a, b)[source]

If coordinates have changed significantly then cutoff lists should be updated.

update_prev_coords(coords)[source]

Rewriting previous coordinates.

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